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Phylogeny and strain typing of Escherichia coli, inferred from variation at mononucleotide repeat loci

APPLIED AND ENVIRONMENTAL MICROBIOLOGY 2004年第4期70卷 2464-2473页

作者： Diamant, E Palti, Y Gur-Arie, R Cohen, H Hallerman, EM Kashi, Y Technion Israel Inst Technol Dept Food Engn & Biotechnol IL-32000 Haifa Israel

Multilocus sequencing of housekeeping genes has been used previously for bacterial strain typing and for inferring evolutionary relationships among strains of Escherichia coli. In this study, we used shorter intergenic sequences that contained simple sequence repeats (SSRs) of repeating mononucleotide motifs (mononucleotide repeats [MNRs]) to infer the phylogeny of pathogenic and commensal E. coli strains. Seven noncoding loci (four MNRs and three non-SSRs) were sequenced in 27 strains, including enterohemorrhagic (six isolates of O157:117), enteropathogenic, enterotoxigenic, B, and K-12 strains. The four MNRs were also sequenced in 20 representative strains of the E. coli reference (ECOR) collection. Sequence pollymorphism was significantly higher at the MNR loci, including the flanking sequences, indicating a higher mutation rate in the sequences flanking the MNR tracts. The four MNR loci were amplifiable by PCR in the standard ECOR A, B1, and D groups, but only one (yaiN) in the B2 group was amplified, which is consistent with previous studies that suggested that B2 is the most ancient group. High sequence compatibility was found between the four MNR loci, indicating that they are in the same clonal frame. The phylogenetic trees that were constructed from the sequence data were in good agreement with those of previous studies that used multilocus enzyme electrophoresis. The results demonstrate that MNR loci are useful for inferring phylogenetic relationships and provide much higher sequence variation than housekeeping genes. Therefore, the use of MNR loci for multilocus sequence typing should prove efficient for clinical diagnostics, epidemiology, and evolutionary study of bacteria.

关键词： .sequences RELATIONSHIPS Multilocus repeats MNRs coli strains noncoding

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Genome-wide evolution analysis reveals low CpG contents of fast-evolving genes and identifies antiviral microRNAs

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Journal of Genetics and Genomics 2020年第1期47卷 49-60页

作者： Wenhong Zu Hang Zhang Xun Lan Xu Tan MOE Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical Biology School of Pharmaceutical SciencesTsinghua UniversityBeijing100084China Beijing Advanced Innovation Center for Structural Biology.Beijing Frontier Research Center for Biological Structures Tsinghua UniversityBeijing100084China Department of Basic Medical Sciences School of MedicineTsinghua UniversityBeijing100084China Center for Infectious Disease Research Tsinghua UniversityBeijing100084China Tsinghua-Peking Center for Life Sciences Beijing100084China

noncoding RNAs(ncRNAs) play important roles in many biological processes and provide materials for evolutionary adaptations beyond protein-coding genes, such as in the arms race between the host and pathogen. However, currently, a comprehensive high-resolution analysis of primate genomes that includes the latest annotated ncRNAs is not available. Here, we developed a computational pipeline to estimate the selections that act on noncoding regions based on comparisons with a large number of reference sequences in introns adjacent to the interested regions. Our method yields result comparable with those of the established codon-based method and phyloP method for coding genes;thus, it provides a holistic framework for estimating the selection on the entire genome. We further showed that fastevolving protein-coding genes and their corresponding 50 UTRs have a significantly lower frequency of the CpG dinucleotides than those evolving at an average pace, and these fast-evolving genes are enriched in the process of immunity and host defense. We also identified fast-evolving miRNAs with antiviral functions in cells. Our results provide a resource for high-resolution evolution analysis of the primate genomes.

关键词： Host-virus interaction Positive selection CpG dinucleotide noncoding RNA MicroRNA

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MiPepid: MicroPeptide identification tool using machine learning

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BMC BIOINFORMATICS 2019年第1期20卷 1-11页

作者： Zhu, Mengmeng Gribskov, Michael Purdue Univ Dept Stat W Lafayette IN 47907 USA Purdue Univ Dept Biol Sci W Lafayette IN 47907 USA

Background Micropeptides are small proteins with length < = 100 amino acids. Short open reading frames that could produces micropeptides were traditionally ignored due to technical difficulties, as few small peptides had been experimentally confirmed. In the past decade, a growing number of micropeptides have been shown to play significant roles in vital biological activities. Despite the increased amount of data, we still lack bioinformatics tools for specifically identifying micropeptides from DNA sequences. Indeed, most existing tools for classifying coding and noncoding ORFs were built on datasets in which "normal-sized" proteins were considered to be positives and short ORFs were generally considered to be noncoding. Since the functional and biophysical constraints on small peptides are likely to be different from those on "normal" proteins, methods for predicting short translated ORFs must be trained independently from those for longer proteins. Results In this study, we have developed MiPepid, a machine-learning tool specifically for the identification of micropeptides. We trained MiPepid using carefully cleaned data from existing databases and used logistic regression with 4-mer features. With only the sequence information of an ORF, MiPepid is able to predict whether it encodes a micropeptide with 96% accuracy on a blind dataset of high-confidence micropeptides, and to correctly classify newly discovered micropeptides not included in either the training or the blind test data. Compared with state-of-the-art coding potential prediction methods, MiPepid performs exceptionally well, as other methods incorrectly classify most bona fide micropeptides as noncoding. MiPepid is alignment-free and runs sufficiently fast for genome-scale analyses. It is easy to use and is available at . Conclusions MiPepid was developed to specifically predict micropeptides, a category of proteins with increasing significance, from DNA sequences. It shows evident advantages over exis

关键词： Micropeptide Small ORF sORF smORF Coding noncoding lncRNA Machine learning

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Long non-coding RNAs involved in metastasis of gastric cancer

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World Journal of Gastroenterology 2018年第33期24卷 3724-3737页

作者： Meng-Ting Lin Hao-Jun Song Xiao-Yun Ding Medical School of Ningbo University Ningbo 315000Zhejiang ProvinceChina Gastroenterology Department Ningbo First HospitalNingbo 315000Zhejiang ProvinceChina

Gastric cancer(GC) is one of the most frequently diagnosed malignant diseases. The molecular mechanisms of metastasis remain unclear. Recently, studies have shown that long non-coding RNAs(lncRNAs) play critical roles in metastasis. Therefore, deeper understanding of this mechanism could provide potential diagnostic tools and therapeutic targets for metastatic GC. This review focuses on dysregulated lncRNAs in GC metastases. Due to the identification of multiple diverse mechanisms involved in GC metastasis, we classified them into seven categories, including lncRNAs related to epithelialmesenchymal transition, regulation of degradation of extracellular matrix, angiopoiesis, vasculogenic mimicry, and immunologic escape. As the TNM stage is pivotal for evaluating the severity and prognosis of GC patients, we summarize the lncRNAs relevant to lymphatic metastasis, distant metastasis and TNM classification. This review summarizes the lncRNAs related to metastasis, which may provide insight into the mechanisms, and provide potential markers for prognostic prediction and monitoring the relapse of GC.

关键词： Long noncoding RNAs Stomach neoplasms Metastasis

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Linc00675 is a novel marker of short survival and recurrence in patients with pancreatic ductal adenocarcinoma

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World Journal of Gastroenterology 2015年第31期21卷 9348-9357页

作者： Dou-Dou Li Zhi-Qiang Fu Qing Lin Yu Zhou Quan-Bo Zhou Zhi-Hua Li Lang-Ping Tan Ru-Fu Chen Yi-Min Liu Department of Radiotherapy Sun Yatsen Memorial HospitalSun Yat-sen University Department of Pancreaticobiliary and Hepatobiliary Surgery Sun Yat-sen Memorial HospitalSun Yat-sen University Department of Medical Oncology Sun Yat-sen Memorial HospitalSun Yat-sen University

AIM: To detect linc00675 expression in pancreatic ductal adenocarcinoma(PDAC),to analyze the relationship between the expression level of linc00675 and the clinical pathological characteristics,to explore the biological functions of linc00675,and to determine whether linc00675 has independent prognostic value in ***: We studied linc00675 expression among eight histologically confirmed PDAC tissue samples and four chronic pancreatitis tissue samples through microarray screening. RT-q PCR was conducted to further investigate linc00675 expression in PDAC cell lines as well as archived tissues from a large cohort of PDAC patients. The correlations between the level of lnc00675 and clinicopathological characteristics and survival in patients with pancreatic cancer were evaluated using Correlation analysis. Univariate andmultivariate analyses were conducted to predict whether lnc00675 expression is an independent prognostic and recurrence factor in patients with pancreatic cancer. After downregulating the expression of linc00675 through si RNA,MTT assay,flow cytometry,transwell assay and Western blot were used to explore the biological function of linc00675 in proliferation,invasion,and cell cycle progression of pancreatic cancer cells. The relative molecular expression levels of epithelial-mesenchymal transition were determined by reverse transcription-polymerase chain reaction(RT-PCR) and Western ***: The expression of Linc00675 in PDAC tissue samples was shown to be 672 times that in chronic pancreatitis tissue samples by microarray screening(P = 3.69 × 10-5). This finding was confirmed in tumor tissues from 90 patients with PDAC compared with adjacent normal tissue samples by quantitative RTPCR. We found that linc00675 overexpression positively correlated with lymph node metastasis(P = 0.005),perineural invasion(P = 0.006),and poor survival(P < 0.001). Univariate and multivariate analyses showed that linc00675 expression served as an independent pred

关键词： Linc00675 Long noncoding RNAs Pro-gnosis biomarker

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Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster

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GENETICS 2005年第2期169卷 709-722页

作者： Singh, ND Arndt, PF Petrov, DA Stanford Univ Dept Biol Sci Stanford CA 94305 USA Max Planck Inst Mol Genet D-14195 Berlin Germany

Mutation is the underlying force that provides the variation upon which evolutionary forces can act. It is important to understand how mutation rates vary within genomes and how the probabilities of fixation of new mutations vary as well. If substitutional processes across the genome are heterogeneous, then examining patterns of coding sequence evolution without taking these underlying variations into account may be misleading. Here we present the first rigorous test of substitution rate heterogeneity in the Drosophila melanogaster genome using almost 1500 nonfunctional fragments of the transposable element DNAREP1_DM. Not only do our analyses suggest that substitutional patterns in heterochromatic and euchromatic sequences are different, but also they provide support in favor of a recombination-associated substitutional bias toward G and C in this species. The magnitude of this bias is entirely sufficient to explain recombination-associated patterns of codon usage on the autosomes of the D. melanogaster genome. We also document a bias toward lower GC content in the pattern of small insertions and deletions (indels). In addition, the GC content of noncoding DNA in Drosophila is higher than would be predicted on the basis of the pattern of nucleoticle substitutions and small indels. However, we argue that the fast turnover of noncoding sequences in Drosophila makes it difficult to assess the importance of the GC biases in nucleotide substitutions and small indels in shaping the base composition of noncoding sequences.

关键词： .toward noncoding substitutions heterogeneity codon autosomes Usage probabilities heterochromatic transposable element euchromatic GC content melanogaster genome Patterns in Drosophila DNAREP substitutional bias

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A Novel Test for Selection on cis-Regulatory Elements Reveals Positive and Negative Selection Acting on Mammalian Transcriptional Enhancers

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MOLECULAR BIOLOGY AND EVOLUTION 2013年第11期30卷 2509-2518页

作者： Smith, Justin D. McManus, Kimberly F. Fraser, Hunter B. Stanford Univ Dept Genet Stanford CA 94305 USA Stanford Univ Dept Biol Stanford CA 94305 USA

Measuring natural selection on genomic elements involved in the cis-regulation of gene expression-such as transcriptional enhancers and promoters-is critical for understanding the evolution of genomes, yet it remains a major challenge. Many studies have attempted to detect positive or negative selection in these noncoding elements by searching for those with the fastest or slowest rates of evolution, but this can be problematic. Here, we introduce a new approach to this issue, and demonstrate its utility on three mammalian transcriptional enhancers. Using results from saturation mutagenesis studies of these enhancers, we classified all possible point mutations as upregulating, downregulating, or silent, and determined which of these mutations have occurred on each branch of a phylogeny. Applying a framework analogous to K-a/K-s in protein-coding genes, we measured the strength of selection on upregulating and downregulating mutations, in specific branches as well as entire phylogenies. We discovered distinct modes of selection acting on different enhancers: although all three have experienced negative selection against downregulating mutations, the selection pressures on upregulating mutations vary. In one case, we detected positive selection for upregulation, whereas the other two had no detectable selection on upregulating mutations. Our methodology is applicable to the growing number of saturation mutagenesis data sets, and provides a detailed picture of the mode and strength of natural selection acting on cis-regulatory elements.

关键词： natural selection noncoding enhancer neutral cis-regulation

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Circular RNAs in physiology and non-immunological diseases

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TRENDS IN BIOCHEMICAL SCIENCES 2022年第3期47卷 250-264页

作者： Chen, Liang Huang, Chuan Shan, Ge Univ Sci & Technol China UTSC Chinese Acad Sci CAS Key Lab Innate Immun & Chron Div Life Sci & MedAffiliated Hosp USTC 1 Sch Basic Med SciDept Clin LabHefei Natl Lab Ph Hefei 230027 Peoples R China Chongqing Univ Sch Life Sci Chongqing 401331 Peoples R China Chongqing Univ Ctr Plant Funct Genom Inst Adv Interdisciplinary Studies Chongqing 401331 Peoples R China Zhejiang Univ Sch Med Sir Run Run Shaw Hosp Hangzhou 310016 Peoples R China

Circular RNAs (circRNAs) are covalently closed single-stranded RNAs. Four subclasses of circRNAs have been identified in animal cells, and they have unique features in their biogenesis, degradation, and transport. CircRNAs have diverse molecular functions in sponging miRNAs, regulating transcription, modulating RNA-binding proteins, and even encoding proteins. Some circRNAs are important regulators of various physiological processes to maintain homeostasis. Dysregulation of circRNAs is associated with human disorders, and individual circRNAs are crucial factors that contribute to major diseases including non-immunological diseases such as cancers, neurological disorders, cardiovascular disease, and metabolic disease. Debates on circRNAs have also been raised in recent years, and further studies would help to resolve these disputes and potentially lead to biomedical applications of circRNAs.

关键词： RNA homeostasis molecular mechanism pathology coding noncoding

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Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test

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GENETICS IN MEDICINE 2018年第4期20卷 435-443页

作者： Lionel, Anath C. Costain, Gregory Monfared, Nasim Walker, Susan Reuter, Miriam S. Hosseini, S. Mohsen Thiruvahindrapuram, Bhooma Merico, Daniele Jobling, Rebekah Nalpathamkalam, Thomas Pellecchia, Giovanna Sung, Wilson W. L. Wang, Zhuozhi Bikangaga, Peter Boelman, Cyrus Carter, Melissa T. Cordeiro, Dawn Cytrynbaum, Cheryl Dell, Sharon D. Dhir, Priya Dowling, James J. Heon, Elise Hewson, Stacy Hiraki, Linda Inbar-Feigenberg, Michal Klatt, Regan Kronick, Jonathan Laxer, Ronald M. Licht, Christoph MacDonald, Heather Mercimek-Andrews, Saadet Mendoza-Londono, Roberto Piscione, Tino Schneider, Rayfel Schulze, Andreas Silverman, Earl Siriwardena, Komudi Snead, O. Carter Sondheimer, Neal Sutherland, Joanne Vincent, Ajoy Wasserman, Jonathan D. Weksberg, Rosanna Shuman, Cheryl Carew, Chris Szego, Michael J. Hayeems, Robin Z. Basran, Raveen Stavropoulos, Dimitri J. Ray, Peter N. Bowdin, Sarah Meyn, M. Stephen Cohn, Ronald D. Scherer, Stephen W. Marshall, Christian R. Hosp Sick Children Ctr Appl Genom Toronto ON Canada Hosp Sick Children Program Genet & Genome Biol Toronto ON Canada Hosp Sick Children Div Clin & Metab Genet Toronto ON Canada Hosp Sick Children Ctr Genet Med Toronto ON Canada Hosp Sick Children Cardiac Genome Clin Ted Rogers Ctr Heart Res Toronto ON Canada Deep Genom Inc Toronto ON Canada Hosp Sick Children Dept Paediat Lab Med Genome Diagnost Toronto ON Canada William Osler Hlth Ctr Brampton ON Canada Hosp Sick Children Div Resp Med Toronto ON Canada BC Childrens Hosp Div Neurol Vancouver BC Canada Childrens Hosp Eastern Ontario Reg Genet Program Ottawa ON Canada Univ Toronto Dept Mol Genet Toronto ON Canada Hosp Sick Children Child Hlth Evaluat Sci Toronto ON Canada Univ Toronto Dept Paediat Toronto ON Canada Hosp Sick Children Div Neurol Toronto ON Canada Hosp Sick Children Department Ophthalmol & Vis Sci Toronto ON Canada Hosp Sick Children Div Rheumatol Toronto ON Canada Hosp Sick Children Div Nephrol Toronto ON Canada Hosp Sick Children Program Cell Biol Toronto ON Canada Hosp Sick Children Program Physiol & Expt Med Toronto ON Canada Univ Alberta Dept Med Genet Edmonton AB Canada Hosp Sick Children Div Endocrinol Toronto ON Canada St Josephs Hlth Ctr Ctr Clin Eth Toronto ON Canada Univ Toronto Joint Ctr Bioeth Toronto ON Canada Univ Toronto Dept Family & Community Med Toronto ON Canada Univ Toronto Dalla Lana Sch Publ Hlth Toronto ON Canada Univ Toronto Inst Hlth Policy Management & Evaluat Toronto ON Canada Univ Toronto Lab Med & Pathobiol Toronto ON Canada

Purpose: Genetic testing is an integral diagnostic component of pediatric medicine. Standard of care is often a time-consuming stepwise approach involving chromosomal microarray analysis and targeted gene sequencing panels, which can be costly and inconclusive. Whole-genome sequencing (WGS) provides a comprehensive testing platform that has the potential to streamline genetic assessments, but there are limited comparative data to guide its clinical use.& para;& para;Methods: We prospectively recruited 103 patients from pediatric non-genetic subspecialty clinics, each with a clinical phenotype suggestive of an underlying genetic disorder, and compared the diagnostic yield and coverage of WGS with those of conventional genetic testing.& para;& para;Results: WGS identified diagnostic variants in 41% of individuals, representing a significant increase over conventional testing results (24%;P = 0.01). Genes clinically sequenced in the cohort (n = 1,226) were well covered by WGS, with a median exonic coverage of 40 x +/- 8 x (mean +/- SD). All the molecular diagnoses made by conventional methods were captured by WGS. The 18 new diagnoses made with WGS included structural and non-exonic sequence variants not detectable with whole-exome sequencing, and confirmed recent disease associations with the genes PIGG, RNU4ATAC, TRIO, and UNC13A.& para;& para;Conclusion: WGS as a primary clinical test provided a higher diagnostic yield than conventional genetic testing in a clinically heterogeneous cohort.

关键词： copy number variation next-generation sequencing noncoding diagnostics whole-genome sequencing

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GENOME OF COXSACKIEVIRUS-B3

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VIROLOGY 1987年第1期156卷 50-63页

作者： LINDBERG, AM STALHANDSKE, POK PETTERSSON, U UNIV UPPSALA CTR BIOMED DEPT MED GENET & MICROBIOL BOX 589 S-75123 UPPSALA SWEDEN

The entire nucleotide sequence of the coxsackievirus B3 strain Nancy (CB3) genome has been determined from cDNA. The genome is 7396 nucleotides long, and encodes a 2185 amino acid long polyprotein. It exhibits the same gene organization as other enterovirus genomes. A detailed comparison was carried out between the proteins encoded by the CB3 and poliovirus type 1 strain Mahoney (PV1) genomes. The genes encoding the VPg polypeptide and the viral polymerase are the most conserved regions. The structural polypeptides VP1, VP2, and VP3 are less well conserved although proline and tryptophan residues frequently are found in identical positions. The VP1 protein of CB3 shows a particularly limited homology in those regions which have been found to induce neutralizing antibodies against PV1. The 5'' noncoding region of CB3 is closely related to that of PV1, with regard to both length and sequence organization, whereas the 3'' noncoding region of CB3 exhibits some unique features.

关键词： aa amino acid CB Coxsackievirus group B HRV human rhinovirus nc noncoding nt nucleotide PV poliovirus

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